Distinct domestication trajectories in top-fermenting beer yeasts and wine yeasts

Beer is one of the oldest alcoholic beverages and is produced by the fermentation of sugars derived from starches present in cereal grains. Contrary to lager beers, ale beers are closer to the ancient beer type and are fermented by Saccharomyces cerevisiae whose cells tend to remain in suspension, being therefore designated as “top-fermenting” yeasts. Here we use population genomics to investigate (i) what are the closest relatives of top-fermenting beer yeasts; (ii) whether top-fermenting yeasts represent an independent domestication event separate those already described; (iii) if single or multiple domestication events can be inferred for top-fermenting yeasts and if (iv) top-fermenting yeasts represent clean or recombinant lineages. Our results revealed that top-fermenting beer yeasts are polyphyletic with a main clade composed of at least three subgroups, dominantly represented by the German, British and wheat beers. Moreover, other beer strains were found to be phylogenetically close to either sake, wine or bread yeasts. Specific genetic signatures of the domestication of beer yeasts were found and we propose that the emergence of the main clade of beer yeasts is related with a domestication event distinct from the previously known cases of wine and sake yeast domestication. The nucleotide diversity of the main Beer clade more than doubled that previously observed for wine yeasts, which might be a consequence of the fundamental differences in the modes of beer and wine domestication. The higher diversity of beer strains could be due to a more intense artificial selection and to different selection regimes related to the development of distinct beers.